Literature DB >> 19423393

varDB: common ground for a shifting landscape.

David R Allred1, Anthony F Barbet, J David Barry, Kirk W Deitsch.   

Abstract

Antigenic variation is a phylogenetically widespread phenomenon thought to lead to survival benefits for the pathogen. Although governed by genetic mechanisms, antigenic variation is ultimately manifested in variant proteins. The varDB database is an attempt to gain an overview of common structures and functions of variant proteins related to enhanced survival. varDB provides a wealth of sequence data and several tools to facilitate their analysis, but current limitations preclude achievement of its full promise. A critique of this database and how it could serve the scientific community is provided here.

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Year:  2009        PMID： 19423393      PMCID： PMC3697053          DOI： 10.1016/j.pt.2009.03.003

Source DB:  PubMed          Journal:  Trends Parasitol        ISSN： 1471-4922


  27 in total

1.  Superinfection as a driver of genomic diversification in antigenically variant pathogens.

Authors:  James E Futse; Kelly A Brayton; Michael J Dark; Donald P Knowles; Guy H Palmer
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-05       Impact factor: 11.205

2.  The ves multigene family of B. bovis encodes components of rapid antigenic variation at the infected erythrocyte surface.

Authors:  D R Allred; J M Carlton; R L Satcher; J A Long; W C Brown; P E Patterson; R M O'Connor; S E Stroup
Journal:  Mol Cell       Date:  2000-01       Impact factor: 17.970

3.  Identification of 19 polymorphic major outer membrane protein genes and their immunogenic peptides in Ehrlichia ewingii for use in a serodiagnostic assay.

Authors:  Chunbin Zhang; Qingming Xiong; Takane Kikuchi; Yasuko Rikihisa
Journal:  Clin Vaccine Immunol       Date:  2007-12-19

4.  Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

Authors:  Jane M Carlton; John H Adams; Joana C Silva; Shelby L Bidwell; Hernan Lorenzi; Elisabet Caler; Jonathan Crabtree; Samuel V Angiuoli; Emilio F Merino; Paolo Amedeo; Qin Cheng; Richard M R Coulson; Brendan S Crabb; Hernando A Del Portillo; Kobby Essien; Tamara V Feldblyum; Carmen Fernandez-Becerra; Paul R Gilson; Amy H Gueye; Xiang Guo; Simon Kang'a; Taco W A Kooij; Michael Korsinczky; Esmeralda V-S Meyer; Vish Nene; Ian Paulsen; Owen White; Stuart A Ralph; Qinghu Ren; Tobias J Sargeant; Steven L Salzberg; Christian J Stoeckert; Steven A Sullivan; Marcio M Yamamoto; Stephen L Hoffman; Jennifer R Wortman; Malcolm J Gardner; Mary R Galinski; John W Barnwell; Claire M Fraser-Liggett
Journal:  Nature       Date:  2008-10-09       Impact factor: 49.962

5.  Analysis of the VSG gene silent archive in Trypanosoma brucei reveals that mosaic gene expression is prominent in antigenic variation and is favored by archive substructure.

Authors:  Lucio Marcello; J David Barry
Journal:  Genome Res       Date:  2007-07-25       Impact factor: 9.043

6.  varDB: a pathogen-specific sequence database of protein families involved in antigenic variation.

Authors:  C Nelson Hayes; Diego Diez; Nicolas Joannin; Wataru Honda; Minoru Kanehisa; Mats Wahlgren; Craig E Wheelock; Susumu Goto
Journal:  Bioinformatics       Date:  2008-09-06       Impact factor: 6.937

7.  VSGdb: a database for trypanosome variant surface glycoproteins, a large and diverse family of coiled coil proteins.

Authors:  Lucio Marcello; Suraj Menon; Pauline Ward; Jonathan M Wilkes; Nicola G Jones; Mark Carrington; J David Barry
Journal:  BMC Bioinformatics       Date:  2007-05-02       Impact factor: 3.169

8.  The Pfam protein families database.

Authors:  Robert D Finn; John Tate; Jaina Mistry; Penny C Coggill; Stephen John Sammut; Hans-Rudolf Hotz; Goran Ceric; Kristoffer Forslund; Sean R Eddy; Erik L L Sonnhammer; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2007-11-26       Impact factor: 16.971

9.  Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa.

Authors:  Kelly A Brayton; Audrey O T Lau; David R Herndon; Linda Hannick; Lowell S Kappmeyer; Shawn J Berens; Shelby L Bidwell; Wendy C Brown; Jonathan Crabtree; Doug Fadrosh; Tamara Feldblum; Heather A Forberger; Brian J Haas; Jeanne M Howell; Hoda Khouri; Hean Koo; David J Mann; Junzo Norimine; Ian T Paulsen; Diana Radune; Qinghu Ren; Roger K Smith; Carlos E Suarez; Owen White; Jennifer R Wortman; Donald P Knowles; Terry F McElwain; Vishvanath M Nene
Journal:  PLoS Pathog       Date:  2007-10-19       Impact factor: 6.823

10.  A histone methyltransferase modulates antigenic variation in African trypanosomes.

Authors:  Luisa M Figueiredo; Christian J Janzen; George A M Cross
Journal:  PLoS Biol       Date:  2008-07-01       Impact factor: 8.029
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